<span style>Hi Mark, </span><div style><br></div><div style>Thanks for your reply! I'm sorry, you're right, as far as I know the manual doesn't actually mention Buckingham pairs generation... but when I set gen-pairs to "yes" and run grompp, I get the following error: </div>
<div style><div><br></div><div>"Generating pair parameters is only supported with LJ non-bonded interactions"</div></div><div style><br></div><div style>I guess I'm wondering how anyone can use the Buckingham potential at all, since Gromacs does not appear to support pairs generation for the Buckingham or the use of explicitly defined Buckingham pair parameters (when defining [ pairtypes ], you have to give the parameters in LJ form). </div>
<div style><br></div><div style>Thanks so much again,</div><div style>Olivia</div><br class="Apple-interchange-newline"><br><div class="gmail_quote">On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><div> </div><div> </div><span>On 29/12/11, <b>Olivia Waring </b><<a href="mailto:owaring@princeton.edu" target="_blank">owaring@princeton.edu</a>> wrote:</span>
<blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">I apologize for the truncated message; I pressed send too soon.
<div><br></div><div>According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential,</div></blockquote>
<div> </div></div><div>Where does it say this?</div><div class="im"><div> </div><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue?</blockquote>
<div> </div></div><div>You want a 1-4 interaction using Buckingham functional form? If so, I don't think GROMACS supports it. If you're trying to combine bits of force fields that use L-J with bits of force fields that use Buckingham, then that's almost certainly a bad idea.</div>
<span class="HOEnZb"><font color="#888888"><div> </div><div>Mark </div></font></span><div class="HOEnZb"><div class="h5"><div> </div><blockquote style="BORDER-LEFT:#00f 1px solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">
<div>
<div> </div><div><br></div><div>Thank you so much,</div><div>Olivia<br><br>
<div class="gmail_quote">On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring <span dir="ltr"><<a href="mailto:owaring@princeton.edu" target="_blank">owaring@princeton.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Hello Gromacs users,
<div><br></div><div>I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file:</div><div><br></div><div>
<div>[ defaults ]</div><div>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ</div><div> 2 1 no 1.0 1.0</div></div><span><font color="#888888">
<div><br></div><div><br><br clear="all">
<div><br></div>-- <br>
<div>Olivia Waring (Íõάæ«)</div><div>Princeton University '12</div><div>AB Chemistry</div><br></div></font></span></blockquote></div><br></div><br clear="all">
<div><br></div>-- <br>
<div>Olivia Waring (Íõάæ«)</div><div>Princeton University '12</div><div>AB Chemistry</div><br></div></blockquote>
<div> </div>
</div></div><br>--<br>
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